PMC:7067204 / 1699-4868 JSON TXT

Annnotations TAB JSON ListView MergeView

LitCovid-PubTator

LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T9","span":{"begin":81,"end":84},"obj":"Body_part"},{"id":"T10","span":{"begin":387,"end":391},"obj":"Body_part"},{"id":"T11","span":{"begin":453,"end":457},"obj":"Body_part"},{"id":"T12","span":{"begin":1063,"end":1067},"obj":"Body_part"},{"id":"T13","span":{"begin":1564,"end":1587},"obj":"Body_part"},{"id":"T14","span":{"begin":1729,"end":1752},"obj":"Body_part"},{"id":"T15","span":{"begin":1879,"end":1884},"obj":"Body_part"},{"id":"T16","span":{"begin":2786,"end":2791},"obj":"Body_part"},{"id":"T17","span":{"begin":3002,"end":3008},"obj":"Body_part"},{"id":"T18","span":{"begin":3074,"end":3081},"obj":"Body_part"}],"attributes":[{"id":"A9","pred":"fma_id","subj":"T9","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A10","pred":"fma_id","subj":"T10","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A11","pred":"fma_id","subj":"T11","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A12","pred":"fma_id","subj":"T12","obj":"http://purl.org/sig/ont/fma/fma24920"},{"id":"A13","pred":"fma_id","subj":"T13","obj":"http://purl.org/sig/ont/fma/fma45662"},{"id":"A14","pred":"fma_id","subj":"T14","obj":"http://purl.org/sig/ont/fma/fma45662"},{"id":"A15","pred":"fma_id","subj":"T15","obj":"http://purl.org/sig/ont/fma/fma7197"},{"id":"A16","pred":"fma_id","subj":"T16","obj":"http://purl.org/sig/ont/fma/fma9576"},{"id":"A17","pred":"fma_id","subj":"T17","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A18","pred":"fma_id","subj":"T18","obj":"http://purl.org/sig/ont/fma/fma84116"}],"text":"Introduction\nCoronaviruses (CoVs) are enveloped, positive-sense, single-stranded RNA viruses that belong to the subfamily Coronavirinae, family Coronavirdiae, order Nidovirales. There are four genera of CoVs, namely, Alphacoronavirus (αCoV), Betacoronavirus (βCoV), Deltacoronavirus (δCoV), and Gammacoronavirus (γCoV) [1]. Evolutionary analyses have shown that bats and rodents are the gene sources of most αCoVs and βCoVs, while avian species are the gene sources of most δCoVs and γCoVs. CoVs have repeatedly crossed species barriers and some have emerged as important human pathogens. The best-known examples include severe acute respiratory syndrome CoV (SARS-CoV) which emerged in China in 2002–2003 to cause a large-scale epidemic with about 8000 infections and 800 deaths, and Middle East respiratory syndrome CoV (MERS-CoV) which has caused a persistent epidemic in the Arabian Peninsula since 2012 [2,3]. In both of these epidemics, these viruses have likely originated from bats and then jumped into another amplification mammalian host [the Himalayan palm civet (Paguma larvata) for SARS-CoV and the dromedary camel (Camelus dromedarius) for MERS-CoV] before crossing species barriers to infect humans.\nPrior to December 2019, 6 CoVs were known to infect human, including 2 αCoV (HCoV-229E and HKU-NL63) and 4 βCoV (HCoV-OC43 [lineage A], HCoV-HKU1 [lineage A], SARS-CoV [lineage B] and MERS-CoV [lineage C]). The βCoV lineage A HCoV-OC43 and HCoV-HKU1 usually cause self-limiting upper respiratory infections in immunocompetent hosts and occasionally lower respiratory tract infections in immunocompromised hosts and elderly [4]. In contrast, SARS-CoV (lineage B βCoV) and MERS-CoV (lineage C βCoV) may cause severe lower respiratory tract infection with acute respiratory distress syndrome and extrapulmonary manifestations, such as diarrhea, lymphopenia, deranged liver and renal function tests, and multiorgan dysfunction syndrome, among both immunocompetent and immunocompromised hosts with mortality rates of ∼10% and ∼35%, respectively [5,6]. On 31 December 2019, the World Health Organization (WHO) was informed of cases of pneumonia of unknown cause in Wuhan City, Hubei Province, China [7]. Subsequent virological testing showed that a novel CoV was detected in these patients. As of 16 January 2020, 43 patients have been diagnosed to have infection with this novel CoV, including two exported cases of mild pneumonia in Thailand and Japan [8,9]. The earliest date of symptom onset was 1 December 2019 [10]. The symptomatology of these patients included fever, malaise, dry cough, and dyspnea. Among 41 patients admitted to a designated hospital in Wuhan, 13 (32%) required intensive care and 6 (15%) died. All 41 patients had pneumonia with abnormal findings on chest computerized tomography scans [10].\nWe recently reported a familial cluster of 2019-nCoV infection in a Shenzhen family with travel history to Wuhan [11]. In the present study, we analyzed a 2019-nCoV complete genome from a patient in this familial cluster and compared it with the genomes of related β CoVs to provide insights into the potential source and control strategies."}

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T2","span":{"begin":723,"end":728},"obj":"Body_part"},{"id":"T3","span":{"begin":1564,"end":1587},"obj":"Body_part"},{"id":"T4","span":{"begin":1570,"end":1587},"obj":"Body_part"},{"id":"T5","span":{"begin":1729,"end":1752},"obj":"Body_part"},{"id":"T6","span":{"begin":1735,"end":1752},"obj":"Body_part"},{"id":"T7","span":{"begin":1879,"end":1884},"obj":"Body_part"},{"id":"T8","span":{"begin":2786,"end":2791},"obj":"Body_part"}],"attributes":[{"id":"A2","pred":"uberon_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/UBERON_0002542"},{"id":"A3","pred":"uberon_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/UBERON_0001558"},{"id":"A4","pred":"uberon_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/UBERON_0000065"},{"id":"A5","pred":"uberon_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/UBERON_0001558"},{"id":"A6","pred":"uberon_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/UBERON_0000065"},{"id":"A7","pred":"uberon_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/UBERON_0002107"},{"id":"A8","pred":"uberon_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/UBERON_0001443"}],"text":"Introduction\nCoronaviruses (CoVs) are enveloped, positive-sense, single-stranded RNA viruses that belong to the subfamily Coronavirinae, family Coronavirdiae, order Nidovirales. There are four genera of CoVs, namely, Alphacoronavirus (αCoV), Betacoronavirus (βCoV), Deltacoronavirus (δCoV), and Gammacoronavirus (γCoV) [1]. Evolutionary analyses have shown that bats and rodents are the gene sources of most αCoVs and βCoVs, while avian species are the gene sources of most δCoVs and γCoVs. CoVs have repeatedly crossed species barriers and some have emerged as important human pathogens. The best-known examples include severe acute respiratory syndrome CoV (SARS-CoV) which emerged in China in 2002–2003 to cause a large-scale epidemic with about 8000 infections and 800 deaths, and Middle East respiratory syndrome CoV (MERS-CoV) which has caused a persistent epidemic in the Arabian Peninsula since 2012 [2,3]. In both of these epidemics, these viruses have likely originated from bats and then jumped into another amplification mammalian host [the Himalayan palm civet (Paguma larvata) for SARS-CoV and the dromedary camel (Camelus dromedarius) for MERS-CoV] before crossing species barriers to infect humans.\nPrior to December 2019, 6 CoVs were known to infect human, including 2 αCoV (HCoV-229E and HKU-NL63) and 4 βCoV (HCoV-OC43 [lineage A], HCoV-HKU1 [lineage A], SARS-CoV [lineage B] and MERS-CoV [lineage C]). The βCoV lineage A HCoV-OC43 and HCoV-HKU1 usually cause self-limiting upper respiratory infections in immunocompetent hosts and occasionally lower respiratory tract infections in immunocompromised hosts and elderly [4]. In contrast, SARS-CoV (lineage B βCoV) and MERS-CoV (lineage C βCoV) may cause severe lower respiratory tract infection with acute respiratory distress syndrome and extrapulmonary manifestations, such as diarrhea, lymphopenia, deranged liver and renal function tests, and multiorgan dysfunction syndrome, among both immunocompetent and immunocompromised hosts with mortality rates of ∼10% and ∼35%, respectively [5,6]. On 31 December 2019, the World Health Organization (WHO) was informed of cases of pneumonia of unknown cause in Wuhan City, Hubei Province, China [7]. Subsequent virological testing showed that a novel CoV was detected in these patients. As of 16 January 2020, 43 patients have been diagnosed to have infection with this novel CoV, including two exported cases of mild pneumonia in Thailand and Japan [8,9]. The earliest date of symptom onset was 1 December 2019 [10]. The symptomatology of these patients included fever, malaise, dry cough, and dyspnea. Among 41 patients admitted to a designated hospital in Wuhan, 13 (32%) required intensive care and 6 (15%) died. All 41 patients had pneumonia with abnormal findings on chest computerized tomography scans [10].\nWe recently reported a familial cluster of 2019-nCoV infection in a Shenzhen family with travel history to Wuhan [11]. In the present study, we analyzed a 2019-nCoV complete genome from a patient in this familial cluster and compared it with the genomes of related β CoVs to provide insights into the potential source and control strategies."}

LitCovid-PD-HP

LitCovid-PD-MONDO

LitCovid-PD-CLO

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T18","span":{"begin":0,"end":12},"obj":"Sentence"},{"id":"T19","span":{"begin":13,"end":177},"obj":"Sentence"},{"id":"T20","span":{"begin":178,"end":323},"obj":"Sentence"},{"id":"T21","span":{"begin":324,"end":490},"obj":"Sentence"},{"id":"T22","span":{"begin":491,"end":588},"obj":"Sentence"},{"id":"T23","span":{"begin":589,"end":914},"obj":"Sentence"},{"id":"T24","span":{"begin":915,"end":1214},"obj":"Sentence"},{"id":"T25","span":{"begin":1215,"end":1421},"obj":"Sentence"},{"id":"T26","span":{"begin":1422,"end":1642},"obj":"Sentence"},{"id":"T27","span":{"begin":1643,"end":2061},"obj":"Sentence"},{"id":"T28","span":{"begin":2062,"end":2212},"obj":"Sentence"},{"id":"T29","span":{"begin":2213,"end":2299},"obj":"Sentence"},{"id":"T30","span":{"begin":2300,"end":2469},"obj":"Sentence"},{"id":"T31","span":{"begin":2470,"end":2530},"obj":"Sentence"},{"id":"T32","span":{"begin":2531,"end":2616},"obj":"Sentence"},{"id":"T33","span":{"begin":2617,"end":2729},"obj":"Sentence"},{"id":"T34","span":{"begin":2730,"end":2827},"obj":"Sentence"},{"id":"T35","span":{"begin":2828,"end":2946},"obj":"Sentence"},{"id":"T36","span":{"begin":2947,"end":3169},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Introduction\nCoronaviruses (CoVs) are enveloped, positive-sense, single-stranded RNA viruses that belong to the subfamily Coronavirinae, family Coronavirdiae, order Nidovirales. There are four genera of CoVs, namely, Alphacoronavirus (αCoV), Betacoronavirus (βCoV), Deltacoronavirus (δCoV), and Gammacoronavirus (γCoV) [1]. Evolutionary analyses have shown that bats and rodents are the gene sources of most αCoVs and βCoVs, while avian species are the gene sources of most δCoVs and γCoVs. CoVs have repeatedly crossed species barriers and some have emerged as important human pathogens. The best-known examples include severe acute respiratory syndrome CoV (SARS-CoV) which emerged in China in 2002–2003 to cause a large-scale epidemic with about 8000 infections and 800 deaths, and Middle East respiratory syndrome CoV (MERS-CoV) which has caused a persistent epidemic in the Arabian Peninsula since 2012 [2,3]. In both of these epidemics, these viruses have likely originated from bats and then jumped into another amplification mammalian host [the Himalayan palm civet (Paguma larvata) for SARS-CoV and the dromedary camel (Camelus dromedarius) for MERS-CoV] before crossing species barriers to infect humans.\nPrior to December 2019, 6 CoVs were known to infect human, including 2 αCoV (HCoV-229E and HKU-NL63) and 4 βCoV (HCoV-OC43 [lineage A], HCoV-HKU1 [lineage A], SARS-CoV [lineage B] and MERS-CoV [lineage C]). The βCoV lineage A HCoV-OC43 and HCoV-HKU1 usually cause self-limiting upper respiratory infections in immunocompetent hosts and occasionally lower respiratory tract infections in immunocompromised hosts and elderly [4]. In contrast, SARS-CoV (lineage B βCoV) and MERS-CoV (lineage C βCoV) may cause severe lower respiratory tract infection with acute respiratory distress syndrome and extrapulmonary manifestations, such as diarrhea, lymphopenia, deranged liver and renal function tests, and multiorgan dysfunction syndrome, among both immunocompetent and immunocompromised hosts with mortality rates of ∼10% and ∼35%, respectively [5,6]. On 31 December 2019, the World Health Organization (WHO) was informed of cases of pneumonia of unknown cause in Wuhan City, Hubei Province, China [7]. Subsequent virological testing showed that a novel CoV was detected in these patients. As of 16 January 2020, 43 patients have been diagnosed to have infection with this novel CoV, including two exported cases of mild pneumonia in Thailand and Japan [8,9]. The earliest date of symptom onset was 1 December 2019 [10]. The symptomatology of these patients included fever, malaise, dry cough, and dyspnea. Among 41 patients admitted to a designated hospital in Wuhan, 13 (32%) required intensive care and 6 (15%) died. All 41 patients had pneumonia with abnormal findings on chest computerized tomography scans [10].\nWe recently reported a familial cluster of 2019-nCoV infection in a Shenzhen family with travel history to Wuhan [11]. In the present study, we analyzed a 2019-nCoV complete genome from a patient in this familial cluster and compared it with the genomes of related β CoVs to provide insights into the potential source and control strategies."}

2_test

{"project":"2_test","denotations":[{"id":"31987001-23770275-27754475","span":{"begin":320,"end":321},"obj":"23770275"},{"id":"31987001-17934078-27754476","span":{"begin":909,"end":910},"obj":"17934078"},{"id":"31987001-25810418-27754477","span":{"begin":911,"end":912},"obj":"25810418"},{"id":"31987001-15613317-27754478","span":{"begin":1639,"end":1640},"obj":"15613317"},{"id":"31987001-12711465-27754479","span":{"begin":2056,"end":2057},"obj":"12711465"},{"id":"31987001-27572168-27754480","span":{"begin":2058,"end":2059},"obj":"27572168"}],"text":"Introduction\nCoronaviruses (CoVs) are enveloped, positive-sense, single-stranded RNA viruses that belong to the subfamily Coronavirinae, family Coronavirdiae, order Nidovirales. There are four genera of CoVs, namely, Alphacoronavirus (αCoV), Betacoronavirus (βCoV), Deltacoronavirus (δCoV), and Gammacoronavirus (γCoV) [1]. Evolutionary analyses have shown that bats and rodents are the gene sources of most αCoVs and βCoVs, while avian species are the gene sources of most δCoVs and γCoVs. CoVs have repeatedly crossed species barriers and some have emerged as important human pathogens. The best-known examples include severe acute respiratory syndrome CoV (SARS-CoV) which emerged in China in 2002–2003 to cause a large-scale epidemic with about 8000 infections and 800 deaths, and Middle East respiratory syndrome CoV (MERS-CoV) which has caused a persistent epidemic in the Arabian Peninsula since 2012 [2,3]. In both of these epidemics, these viruses have likely originated from bats and then jumped into another amplification mammalian host [the Himalayan palm civet (Paguma larvata) for SARS-CoV and the dromedary camel (Camelus dromedarius) for MERS-CoV] before crossing species barriers to infect humans.\nPrior to December 2019, 6 CoVs were known to infect human, including 2 αCoV (HCoV-229E and HKU-NL63) and 4 βCoV (HCoV-OC43 [lineage A], HCoV-HKU1 [lineage A], SARS-CoV [lineage B] and MERS-CoV [lineage C]). The βCoV lineage A HCoV-OC43 and HCoV-HKU1 usually cause self-limiting upper respiratory infections in immunocompetent hosts and occasionally lower respiratory tract infections in immunocompromised hosts and elderly [4]. In contrast, SARS-CoV (lineage B βCoV) and MERS-CoV (lineage C βCoV) may cause severe lower respiratory tract infection with acute respiratory distress syndrome and extrapulmonary manifestations, such as diarrhea, lymphopenia, deranged liver and renal function tests, and multiorgan dysfunction syndrome, among both immunocompetent and immunocompromised hosts with mortality rates of ∼10% and ∼35%, respectively [5,6]. On 31 December 2019, the World Health Organization (WHO) was informed of cases of pneumonia of unknown cause in Wuhan City, Hubei Province, China [7]. Subsequent virological testing showed that a novel CoV was detected in these patients. As of 16 January 2020, 43 patients have been diagnosed to have infection with this novel CoV, including two exported cases of mild pneumonia in Thailand and Japan [8,9]. The earliest date of symptom onset was 1 December 2019 [10]. The symptomatology of these patients included fever, malaise, dry cough, and dyspnea. Among 41 patients admitted to a designated hospital in Wuhan, 13 (32%) required intensive care and 6 (15%) died. All 41 patients had pneumonia with abnormal findings on chest computerized tomography scans [10].\nWe recently reported a familial cluster of 2019-nCoV infection in a Shenzhen family with travel history to Wuhan [11]. In the present study, we analyzed a 2019-nCoV complete genome from a patient in this familial cluster and compared it with the genomes of related β CoVs to provide insights into the potential source and control strategies."}

MyTest

{"project":"MyTest","denotations":[{"id":"31987001-23770275-27754475","span":{"begin":320,"end":321},"obj":"23770275"},{"id":"31987001-17934078-27754476","span":{"begin":909,"end":910},"obj":"17934078"},{"id":"31987001-25810418-27754477","span":{"begin":911,"end":912},"obj":"25810418"},{"id":"31987001-15613317-27754478","span":{"begin":1639,"end":1640},"obj":"15613317"},{"id":"31987001-12711465-27754479","span":{"begin":2056,"end":2057},"obj":"12711465"},{"id":"31987001-27572168-27754480","span":{"begin":2058,"end":2059},"obj":"27572168"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"Introduction\nCoronaviruses (CoVs) are enveloped, positive-sense, single-stranded RNA viruses that belong to the subfamily Coronavirinae, family Coronavirdiae, order Nidovirales. There are four genera of CoVs, namely, Alphacoronavirus (αCoV), Betacoronavirus (βCoV), Deltacoronavirus (δCoV), and Gammacoronavirus (γCoV) [1]. Evolutionary analyses have shown that bats and rodents are the gene sources of most αCoVs and βCoVs, while avian species are the gene sources of most δCoVs and γCoVs. CoVs have repeatedly crossed species barriers and some have emerged as important human pathogens. The best-known examples include severe acute respiratory syndrome CoV (SARS-CoV) which emerged in China in 2002–2003 to cause a large-scale epidemic with about 8000 infections and 800 deaths, and Middle East respiratory syndrome CoV (MERS-CoV) which has caused a persistent epidemic in the Arabian Peninsula since 2012 [2,3]. In both of these epidemics, these viruses have likely originated from bats and then jumped into another amplification mammalian host [the Himalayan palm civet (Paguma larvata) for SARS-CoV and the dromedary camel (Camelus dromedarius) for MERS-CoV] before crossing species barriers to infect humans.\nPrior to December 2019, 6 CoVs were known to infect human, including 2 αCoV (HCoV-229E and HKU-NL63) and 4 βCoV (HCoV-OC43 [lineage A], HCoV-HKU1 [lineage A], SARS-CoV [lineage B] and MERS-CoV [lineage C]). The βCoV lineage A HCoV-OC43 and HCoV-HKU1 usually cause self-limiting upper respiratory infections in immunocompetent hosts and occasionally lower respiratory tract infections in immunocompromised hosts and elderly [4]. In contrast, SARS-CoV (lineage B βCoV) and MERS-CoV (lineage C βCoV) may cause severe lower respiratory tract infection with acute respiratory distress syndrome and extrapulmonary manifestations, such as diarrhea, lymphopenia, deranged liver and renal function tests, and multiorgan dysfunction syndrome, among both immunocompetent and immunocompromised hosts with mortality rates of ∼10% and ∼35%, respectively [5,6]. On 31 December 2019, the World Health Organization (WHO) was informed of cases of pneumonia of unknown cause in Wuhan City, Hubei Province, China [7]. Subsequent virological testing showed that a novel CoV was detected in these patients. As of 16 January 2020, 43 patients have been diagnosed to have infection with this novel CoV, including two exported cases of mild pneumonia in Thailand and Japan [8,9]. The earliest date of symptom onset was 1 December 2019 [10]. The symptomatology of these patients included fever, malaise, dry cough, and dyspnea. Among 41 patients admitted to a designated hospital in Wuhan, 13 (32%) required intensive care and 6 (15%) died. All 41 patients had pneumonia with abnormal findings on chest computerized tomography scans [10].\nWe recently reported a familial cluster of 2019-nCoV infection in a Shenzhen family with travel history to Wuhan [11]. In the present study, we analyzed a 2019-nCoV complete genome from a patient in this familial cluster and compared it with the genomes of related β CoVs to provide insights into the potential source and control strategies."}

PMC:7067204 / 1699-4868 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7067204 / 1699-4868 JSON TXT